A novel approximation method of CTF amplitude correction for 3D single particle reconstruction

Ultramicroscopy

Volumn 110, Issue 4, 2010, Pages 350-358

  Jiang, Linhua ^a   Liu, Zunfeng ^a   Georgieva, Dilyana ^a   Kuil, Maxim E ^a   Abrahams, Jan Pieter ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

3D reconstruction; CTF correction; Image processing software; Single particle

Indexed keywords

3D RECONSTRUCTION; AMPLITUDE CORRECTION; APPROXIMATION METHODS; ASYMMETRIC STRUCTURES; CONTRAST TRANSFER FUNCTION; CORRECTION IMAGE; CORRECTION METHOD; DATA SETS; HIGH RESOLUTION; HIGHER RESOLUTION; MICROSCOPIC IMAGE; NANO-METER SCALE; NEW APPROACHES; NOISY IMAGE; PIECEWISE CONTINUOUS FUNCTIONS; RECONSTRUCTION SOFTWARE; SINGLE PARTICLE; SINGLE PARTICLE RECONSTRUCTION; SINGLE-PARTICLE ANALYSIS; THREE-DIMENSIONAL RECONSTRUCTION;

APPROXIMATION THEORY; COMPUTER SOFTWARE; IMAGE RECONSTRUCTION; IMAGING SYSTEMS; MEDICAL IMAGING; REPAIR; SIGNAL FILTERING AND PREDICTION; TRANSFER FUNCTIONS;

THREE DIMENSIONAL;

ALGORITHM; AMPLITUDE MODULATION; ARTICLE; CALCULATION; CONTRAST TRANSFER FUNCTION; CONTROLLED STUDY; ELECTRON MICROSCOPY; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE RECONSTRUCTION; INTERMETHOD COMPARISON; THREE DIMENSIONAL IMAGING;

EID: 77649180251     PISSN: 03043991     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ultramic.2010.01.011     Document Type: Article

References (49)

1. Zhou Z.H. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Current Opinion in Structural Biology 18 (2008) 218-228
2. Chiu W., Baker M.L., Jiang W., Dougherty M., and Schmid M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13 (2005) 363-372
3. Thon F. Zur Defokussierungsabhangigkeit des Phasenkontrastes Bei der Elektronenmikroskopischen Abbildung. Zeitschrift fur Naturforschung Part A-Astrophysik Physik und Physikalische Chemie A 21 (1966) 476-478
4. Erickson H.P., and Klug A. Fourier transform of an electron micrograph-effects of defocussing and aberrations, and implications for use of underfocus contrast enhancement. Berichte der Bunsen-Gesellschaft fur Physikalische Chemie 74 (1970) 1129-1137
5. van Heel M., and Keegstra W. Imagic-a fast, flexible and friendly image-analysis software system. Ultramicroscopy 7 (1981) 113-130
6. van Heel M., Harauz G., Orlova E.V., Schmidt R., and Schatz M. A new generation of the IMAGIC image processing system. Journal of Structural Biology 116 (1996) 17-24
7. Frank J., Shimkin B., and Dowse H. Spider-a modular software system for electron image-processing. Ultramicroscopy 6 (1981) 343-357
8. Frank J., Radermacher M., Penczek P., Zhu J., Li Y.H., Ladjadj M., and Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. Journal of Structural Biology 116 (1996) 190-199
9. Sorzano C.O.S., Marabini R., Velazquez-Muriel J., Bilbao-Castro J.R., Scheres S.H.W., Carazo J.M., and Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. Journal of Structural Biology 148 (2004) 194-204
10. Marabini R., Masegosa I.M., SanMartin M.C., Marco S., Fernandez J.J., delaFraga L.G., Vaquerizo C., and Carazo J.M. Xmipp: an image processing package for electron microscopy. Journal of Structural Biology 116 (1996) 237-240
11. Ludtke S.J., Baldwin P.R., and Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. Journal of Structural Biology 128 (1999) 82-97
12. Liang Y.Y., Ke E.Y., and Zhou Z.H. IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. Journal of Structural Biology 137 (2002) II
13. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., and Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Quarterly Reviews of Biophysics 33 (2000) 307-369
14. Zhou Z.H., Hardt S., Wang B., Sherman M.B., Jakana J., and Chiu W. CTF determination of images of ice-embedded single particles using a graphics interface. Journal of Structural Biology 116 (1996) 216-222
15. Huang Z., Baldwin P.R., Mullapudi S., and Penczek P.A. Automated determination of parameters describing power spectra of micrograph images in electron microscopy. Journal of Structural Biology 144 (2003) 79-94
16. Fernandez J.J., Li S., and Crowther R.A. CTF determination and correction in electron cryotomography. Ultramicroscopy 106 (2006) 587-596
17. Velazquez-Muriel J.A., Sorzano C.O.S., Fernandez J.J., and Carazo J.M. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjustment. Ultramicroscopy 96 (2003) II
18. Mallick S.P., Carragher B., Potter C.S., and Kriegman D.J. ACE: automated CTF estimation. Ultramicroscopy 104 (2005) 8-29
19. Sander B., Golas M.M., and Stark H. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. Journal of Structural Biology 142 (2003) 392-401
20. Thon F. In: Valdre U. (Ed). Phase Contrast Electron Microscopy (1971), Electron Microscopy in Materials Science Academic Press, New York 570-625
21. Hanszen K.J. The optical transfer theory of the electron microscope: fundamental principles and applications. In: Barer R., and Cosslett V.E. (Eds). Advances in Optical and Electron Microscopy (1971) 1-84
22. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies (1996), Academic Press, San Diego
23. Ramachandran G.N., and Srinivasan R. Fourier Methods in Crystallography (1970), Wiley, New York pp. 60-71
24. Grigorieff N. FREALIGN: high-resolution refinement of single particle structures. Journal of Structural Biology 157 (2007) 117-125
25. Sorzano C.O.S., Marabini R., Herman G.T., Censor Y., and Carazo J.M. Transfer function restoration in 3D electron microscopy via iterative data refinement. Physics in Medicine and Biology 49 (2004) DOI
26. Yi Wan W.C., and Zhou Z.H. Full contrast transfer function correction in 3D cryo-EM reconstruction. International Conference on Communications, Circuits and Systems 2 (2004) 960-964
27. Zubelli J.P., Marabini R., Sorzano C.O.S., and Herman G.T. Three-dimensional reconstruction by Chahine's method from electron microscopic projections corrupted by instrumental aberrations. Inverse Problems 19 (2003) II
28. Zhu J., Penczek P.A., Schroder R., and Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. Journal of Structural Biology 118 (1997) 197-219
29. Frank J., and Penczek P. On the correction of the contrast transfer-function in biological electron-microscopy. Optik 98 (1995) 125-129
30. Medipix, 〈http://medipix.web.cern.ch/MEDIPIX/〉.
31. Plaisier J.R., Koning R.I., Koerten H.K., van Roon A.M., Thomassen E.A.J., Kuil M.E., Hendrix J., Broennimann C., Pannu N.S., and Abrahams J.P. Area detectors in structural biology. Nuclear Instruments & Methods in Physics Research Section A-Accelerators Spectrometers Detectors and Associated Equipment 509 (2003) 274-282
32. Penczek P.A., Zhu J., Schroder R., and Frank J. Three dimensional reconstruction with contrast transfer compensation from defocus series. Scanning Microscopy (1997) 147-154
33. Gonzalez R., Woods R., and Eddins S. Digital Image Processing Using Matlab (2003), Prentice Hall
34. Schiske P. Image processing using additional statistical information about the object. In: Hawkes P. (Ed). Image Processing and Computer-aided Design in Electron Optics (1973), Academic Press, London 82-90
35. Ludtke S.J., Jakana J., Song J.L., Chuang D.T., and Chiu W. A 11.5 Angstrom single particle reconstruction of GroEL using EMAN. Journal of Molecular Biology 314 (2001) 253-262
36. Press W.H., Teukolsky S.A., Vettering W.T., and Flannery B.P. Minimization or maximization of functions. In: Press W.H. (Ed). Numerical Recipes: The Art of Scientific Computing (2007), Cambridge University Press
37. Ludtke S.J., Chen D.H., Song J.L., Chuang D.T., and Chiu W. Seeing GroEL at 6 Angstrom resolution by single particle electron cryornicroscopy. Structure 12 (2004) 1129-1136
38. Hartl F.U. Molecular chaperones in cellular protein folding. Nature 381 (1996) 571-580
39. Braig K., Otwinowski Z., Hegde R., Boisvert D.C., Joachimiak A., Horwich A.L., and Sigler P.B. The crystal-structure of the bacterial chaperonin GroEL at 2.8-Angstrom. Nature 371 (1994) 578-586
40. Stagg S.M., Lander G.C., Quispe J., Voss N.R., Cheng A., Bradlow H., Bradlow S., Carragher B., and Potter C.S. A test-bed for optimizing high-resolution single particle reconstructions. Journal of Structural Biology 163 (2008) 29-39
41. Ludtke S.J., Baker M.L., Chen D.H., Song J.L., Chuang D.T., and Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16 (2008) 441-448
42. Harauz G., and van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik 73 (1986) 146-156
43. Bottcher B., Wynne S.A., and Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386 (1997) 88-91
44. van Heel M., and Schatz M. Fourier shell correlation threshold criteria. Journal of Structural Biology 151 (2005) 250-262
45. Braig K., Adams P.D., and Brunger A.T. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Angstrom resolution. Nature Structural Biology 2 (1995) 1083-1094
46. Jiang L., Schaffitzel C., Bingel-Erlenmeyer R., Ban N., Korber P., Koning R.I., de Geus D.C., Plaisier J.R., and Abrahams J.P. Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15. Journal of Molecular Biology 386 (2009) 1357-1367
47. Plaisier J.R., Jiang L., and Abrahams J.P. Cyclops: new modular software suite for cryo-EM. Journal of Structural Biology 157 (2007) 19-27
48. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25 (2004) 1605-1612
49. Cyttron, 〈http://www.cyttron.org/〉.